Moving microdroplets

ABSTRACT

The movement and mixing of microdroplets through microchannels is described employing microscale devices, comprising microdroplet transport channels, reaction regions, electrophoresis modules, and radiation detectors. The discrete droplets are differentially heated and propelled through etched channels. Electronic components are fabricated on the same substrate material, allowing sensors and controlling circuitry to be incorporated in the same device.

This is a Divisional of application(s) 08/938,689 filed on Sep. 26,1997, now U.S. Pat. No. 6,130,098, which is a continuation-in-part ofapplication 08/888,309, filed on Jul. 3, 1997, now U.S. Pat. No.6,048,734, which is a continuation-in part of application Ser. No.08/529,293, filed on Sep. 15, 1995 now U.S. Pat. No. 6,057,149.

This invention was made with government support awarded by the NationalInstitutes of Health (grant numbers NIH-R01-HG01044 andNIH-R01-HG01406). The government has certain rights in the invention.

FIELD OF THE INVENTION

The present invention relates to movement of microdroplets throughmicrochannels, and more particularly, compositions, devices and methodsto control microdroplet size and movement.

BACKGROUND

The complexity and power of biological reactions has increaseddramatically over the last thirty years. The initial observations of the“hybridization” process, i.e., the ability of two polymers of nucleicacid containing complementary sequences to find each other and annealthrough base pairing interaction, by Marmur and Lane, Proc. Nat. Acad.Sci., U.S.A. 46, 453 (1960) and Doty et al., Proc. Nat. Acad. Sci.,U.S.A. 46, 461 (1960), have been followed by the refinement of thisprocess into an essential tool of modern biology.

Initial hybridization studies, such as those performed by Hayashi etal., Proc. Nat. Acad. Sci., USA. 50, 664 (1963), were formed insolution. Further development led to the immobilization of the targetDNA or RNA on solid supports. With the discovery of specific restrictionendonucleases by Smith and Wilcox, J. Mol. Biol. 51, 379 (1970), itbecame possible to isolate discrete fragments of DNA. Utilization ofimmobilization techniques, such as those described by Southern, J. Mol.Biol. 98, 503 (1975), in combination with restriction enzymes, hasallowed for the identification by hybridization of singly copy genesamong a mass of fractionated, genomic DNA.

In 1977, two methods for DNA sequencing were reported. These were thechemical degradation method of Maxam and Gilbert, Proc. Nat. Acad. Sci.USA. 74:560 (1977) and the enzymatic method of Sanger et al., Proc. Nat.Acad. Sci. USA. 74:5463 (1977). Both methods generate populations ofradiolabeled oligonucledtides which begin at a fixed point and terminaterandomly at a fixed residue or type of residue. These populations areresolved on polyacrylamide gels which allow the discrimination betweenoligonucleotides that differ in length by as little as one nucleotide.

The Maxam and Gilbert method utilizes a fragment of DNA radiolabeled atone end which is partially cleaved in five separate chemical reactions,each of which is specific for a particular base or type of base. Theproducts of these chemical reactions are five populations of labelledmolecules that extend from the labeled end to the site of chemicalcleavage. This method has remained relatively unchanged since itsinitial development. This method works best for DNA sequences that lieless than 250 nucleotides from the labeled end.

In contrast, the Sanger method is capable of sequencing greater than 500nucleotides in a single set of reactions. The Sanger method is anenzymatic reaction that utilizes chain-terminating dideoxynucleotides(ddNTPs). ddNTPs are chain-terminating because they lack a 3′-hydroxylresidue which prevents formation of a phosphodiester bond with thesucceeding deoxyribonucleotide (dNTP). A small amount of one ddNTP isincluded with the four conventional dNTPs in a polymerization reaction.Polymerization or DNA synthesis is catalyzed by a DNA polymerase. Thereis competition between extension of the chain by incorporation of theconventional dNTPs and termination of the chain by incorporation of addNTP. A short oligonucleotide or primer is annealed to a templatecontaining the DNA to be sequenced. The original protocols requiredsingle-stranded DNA templates. The use of double-stranded templates wasreported later. The primer provides a 3′ hydroxyl group which allows thepolymerization of a chain of DNA when a polymerase enzyme and dNTPs areprovided.

The original version of the Sanger method utilized the Klenow fragmentof E. coli DNA polymerase. This enzyme has the polymerization and 3′ to5′ exonuclease activity of the unmodified polymerase but lacks 5′ to 3′exonuclease activity. The Klenow fragment has several limitations whenused for enzymatic sequencing. One limitations is the low processivityof the enzyme, which generates a high background of fragments thatterminate by the random dissociation of the enzyme from the templaterather than by the desired termination due to incorporation of a ddNTP.The low processivity also means that the enzyme cannot be used tosequence nucleotides that appear more than ˜250 nucleotides from the 5′end of the primer. A second limitation is that Klenow cannot efficientlyutilize templates which have homopolymer tracts or regions of highsecondary structure. The problems caused by secondary structure in thetemplate can be minimized by running the polymerization reaction at 55°C.

Improvements to the original Sanger method include the use ofpolymerases other than the Klenow fragment. Reverse transcriptase hasbeen used to sequence templates that have homopolymeric tracts. Reversetranscriptase is somewhat better than the Klenow enzyme at utilizingtemplates containing homopolymer tracts.

The use of a modified T7 DNA polymerase (Sequenase™) was the mostsignificant improvement to the Sanger method. See Sambrook, J. et al.Molecular Cloning, A Laboratory Manual, 2d Ed. Cold Spring HarborLaboratory Press, New York, 13.7-13.9 and Hunkapiller, M. W. (1991)Curr. Op. Gen. Devi. 1:88-92. Sequenase™ is a chemically-modified T7 DNApolymerase has reduced 3′ to 5′ exonuclease activity. Tabor et al.,Proc. Natl. Acad. Sci. U.S.A. 84:4767 (1987). Sequenase™ version 2.0 isa genetically engineered form of the T7 polymerase which completelylacks 3′ to 5′ exonticlease activity. Sequenase™ has a very highprocessivity and high rate of polymerization. It can efficientlyincorporate nucleotide analogs such as dITP and 7-deaza-dGTP which areused to resolve regions of compression in sequencing gels. In regions ofDNA containing a high G+C content, Hoogsteen bond formation can occurwhich leads to compressions in the DNA. These compressions result inaberrant migration patterns of oligonucleotide strands on sequencinggels. Because these base analogs pair weakly with conventionalnucleotides, intrastrand secondary structures are alleviated. Incontrast, Klenow does not incorporate these analogs as efficiently. Themain limitation to the amount of DNA sequence that can be obtained froma single set of chain-termination reactions using Sequenase™ is theresolving power of polyacrylamide gels, not the properties of theenzyme.

The use of Taq DNA polymerase is a more recent addition to theimprovements of the Sanger method. Innis et al., Proc. Natl. Acad. Sci.U.S.A. 85:9436 (1988). Taq polymerase is a thermostable enzyme whichworks efficiently at 70-75° C. The ability to catalyze DNA synthesis atelevated temperature makes Taq polymerase useful for sequencingtemplates which have extensive secondary structures at 37° C. (thestandard temperature used for Klenow and Sequenase™ reactions). Taqpolymerase, like Sequenase™, has a high degree of processivity and likeSequenase 2.0, it lacks 3′ to 5′ nuclease activity.

Methods were also developed for examining single base changes withoutdirect sequencing. These methods allow for the “scanning” of DNAfragments for the presence of mutations or other sequence variation. Forexample, if a mutation of interest happens to fall within a restrictionrecognition sequence, a change in the pattern of digestion can be usedas a diagnostic tool (e.g., restriction fragment length polymorphism[RFLP] analysis).

With the development of these complex and powerful biologicaltechniques, an ambitious project has been undertaken. This project,called the Human Genome Project (HGP), involves the completecharacterization of the archetypal human genome sequence which comprises3×10⁹ DNA nucleotide base pairs. An implicit goal of the project is therecognition that all humans are greater than 99% identical at the DNAsequence level. The differences between people, however, provide theinformation most relevant to individual health care, including potentialestimates of the risk of disease or the response to a specific medicaltreatment. Upon completion of the HGP, a continuing effort of the humangenetics research community will be the examination of differenceswithin populations and of individual variants from the definedarchetype. While the 15-year effort of the HGP represents a definedquantity of DNA data acquisition, the future demand for DNA informationis tied to individual genetic variation and is, therefore, unlimited.

Current DNA genotyping technologies are adequate for the detailedanalysis of samples that range in number from hundreds to thousands peryear. Genotyping projects on the order of millions of assays, however,are beyond the capabilities of today's laboratories because of thecurrent inefficiencies in (i) liquid handling of reagent and DNAtemplate solutions, (ii) measurement of solution volumes, (iii) mixingof reagent and template, (iv) controlled thermal reaction of the mixedsolutions, (v) sample loading onto an electrophoresis gel, and (vi) DNAproduct detection on size-separating gels. What is needed is methodologythat allows for a high-volume of Li biological reactions without theseexisting inefficiencies.

SUMMARY OF THE INVENTION

The present invention relates to movement of microdroplets throughmicrochannels, and more particularly, compositions, devices and methodsto control microdroplet size and movement. The present inventioninvolves microfabrication of microscale devices and reactions inmicroscale devices, and in particular, movement of biological samples inmicrodroplets through microchannels to, for example, initiate biologicalreactions.

The present invention contemplates microscale devices, comprisingmicrodroplet transport channels having hydrophilic and hydrophobicregions, reaction chambers, gas-intake pathways and vents,electrophoresis modules, and detectors, including but not limited toradiation detectors. In some embodiments, the devices further compriseair chambers to internally generate air pressure to split and movemicrodroplets (i.e. “on-chip” pressure generation).

In a preferred embodiment, these elements are microfabricated fromsilicon and glass substrates. The various components are linked (i.e.,in liquid communication) using flow-directing means, including but notlimited to, a flow directing means comprising a surface-tension-gradientmechanism in which discrete droplets are differentially heated andpropelled through etched channels. Electronic components are fabricatedon the same substrate material, allowing sensors and controllingcircuitry to be incorporated in the same device. Since all of thecomponents are made using conventional photolithographic techniques,multi-component devices can be readily assembled into complex,integrated systems.

It is not intended that the present invention be limited by the natureof the reactions carried out in the microscale device. Reactionsinclude, but are not limited to, chemical and biological reactions.Biological reactions include, but are not limited to sequencing,restriction enzyme digests, RFLP, nucleic acid amplification, and gelelectrophoresis. It is also not intended that the invention be limitedby the particular purpose for carrying out the biological reactions. Inone medical diagnostic application, it may be desirable to differentiatebetween a heterozygotic and homozygotic target and, in the latter case,specifying which homozygote is present. Where a given genetic locusmight code for allele A or allele a, the assay allows for thedifferentiation of an AA from an Aa from an aa pair of alleles. Inanother medical diagnostic application, it may be desirable to simplydetect the presence or absence of specific allelic variants of pathogensin a clinical sample. For example, different species or subspecies ofbacteria may have different susceptibilities to antibiotics; rapididentification of the specific species or subspecies present aidsdiagnosis and allows initiation of appropriate treatment.

The present invention contemplates a method for moving microdroplets,comprising: (a) providing a liquid microdroplet disposed within amicrodroplet transport channel etched in silicon, said channel in liquidcommunication with a reaction region via said transport channel andseparated from a microdroplet flow-directing means by a liquid barrier;and (b) conveying said microdroplet in said transport channel to saidreaction region via said microdroplet flow-directing means. It isintended that the present invention be limited by the particular natureof the microdroplet flow-directing means. In one embodiment, itcomprises a series of aluminum heating elements arrayed along saidtransport channel and the microdroplets are conveyed by differentialheating of the microdroplet by the heating elements.

It has been found empirically that the methods and devices of thepresent invention can be used with success when, prior to the conveyingdescribed above the transport channel (or channels) is treated with ahydrophilicity-enhancing compound. It is not intended that the inventionbe limited by exactly when the treatment takes place. Indeed, there issome flexibility because of the long-life characteristics of someenhancing compounds.

It has also been found empirically that the methods and devices of thepresent invention can be used with success when regions of themicrochannel are treated with hydrophobic reagents to create hydrophobicregions. By using defined, hydrophobic regions at definite locations inmicrochannels and using a pressure source, one can split off precisenanoliter volume liquid drops (i.e. microdroplets) and control themotion of those drops though the microchannels.

In one embodiment employing such hydrophobic regions (or “hydrophobicpatches”), the present invention contemplates a method for movingmicrodroplets, comprising: (a) providing microdroplet transport channel(or a device comprising a microdroplet transport channel), said channeli) having one or more hydrophobic regions and ii) in communication witha gas source; (b) introducing liquid into said channel under conditionssuch that said liquid stops at one of said hydrophobic regions so as todefine i) a source of liquid microdroplets disposed within said channeland ii) a liquid-abutting hydrophobic region; and (c) separating adiscrete amount of liquid from said source of liquid microdroplets usinggas from said gas source under conditions such that a microdroplet ofdefined size i) comes in contact with, and ii) moves over, saidliquid-abutting hydrophobic region.

In one embodiment, said gas from said gas source enters said channelfrom a gas-intake pathway in communication with said microdroplettransport channel and exits said channel from a gas vent that is also incommunication with said microdroplet transport channel. It is preferred,in this embodiment, that the introduction of liquid into the channel (asset forth in part b of the above-described method) is such that i) theliquid passes over the gas-intake pathway and ii) the desired size ofthe microdroplet is defined by the distance between the gas-intakepathway and the liquid-abutting hydrophobic region. In this embodiment,introduction of the gas (as set forth in part c of the above-describedmethod) forces the microdroplet to i) pass over the liquid-abuttinghydrophobic region and ii) pass by (but not enter) the gas vent.

In another embodiment employing such hydrophobic regions (or“hydrophobic patches”), the present invention contemplates a method formoving microdroplets, comprising: (a) providing a device comprising amicrodroplet transport channel etched in silicon, said channel i) havingone or more hydrophobic regions and ii) in communication with a gassource; (b) introducing liquid into said channel under conditions suchthat said liquid stops at one of said hydrophobic regions so as todefine i) a source of liquid microdroplets disposed within said channeland ii) a liquid abutting hydrophobic region; and (c) separating adiscrete amount of liquid from said source of liquid microdroplets usinggas from said gas source under conditions such that a microdroplet ofdefined size i) comes in contact with, and ii) moves over, saidliquid-abutting hydrophobic region.

Again, it has been found empirically that there is a need for a liquidbarrier between the liquid in the channels and the electronics of thesilicon chip. A preferred barrier comprises a first silicon oxide layer,a silicon nitride layer, and a second silicon oxide layer.

The present invention further contemplates a method for mergingmicrodroplets comprising: (a) providing first and second liquidmicrodroplets, a liquid microdroplet delivering means, and a device,said device comprising: i) a housing comprised of silicon, ii) first andsecond microdroplet transport channels etched in said silicon andconnecting to form a third transport channel containing a reactionregion, iii) a microdroplet receiving means in liquid communication withsaid reaction region via said transport channels, and iv) microdropletflow-directing means arrayed along said first, second and thirdtransport channels; (b) delivering said first liquid microdroplet viasaid microdroplet delivering means to said first transport channel; (c)delivering said second liquid microdroplet via said microdropletdelivering means to said second transport channel; and (d) conveyingsaid microdroplets in said transport channels to said reaction region insaid third transport channel via said microdroplet flow-directing means,thereby merging said first and second microdroplets to create a mergedmicrodroplet.

In one embodiment, said first microdroplet comprises nucleic acid andsaid second microdroplet comprises a nuclease capable of acting on saidnucleic acid. In this embodiment, it is desirable to enhance the mixingwithin the merged microdroplet. This can be achieved a number of ways.In one embodiment for mixing, after the conveying of step (d), the flowdirection is reversed. It is not intended that the present invention belimited by the nature or number of reversals. If the flow direction ofsaid merged microdroplet is reversed even a single time, this processincreases the mixing of the reactants.

The present invention contemplates a variety of silicon-based,microdroplet transport channel-containing devices. In one embodiment,the device comprises: i) a housing comprised of silicon, ii) amicrodroplet transport channel etched in said silicon, iii) amicrodroplet receiving means in liquid communication with a reactionregion via said transport channels, and iv) a liquid barrier disposedbetween said transport channels and a microdroplet flow-directing means.In one embodiment, the device is assembled in two parts. First, thechannels are etched in any number of configurations. Secondly, thispiece is bonded with a silicon-based chip containing the electronics.This allows for both customization (in the first piece) andstandardization (in the second piece).

The present invention also contemplates devices and methods for thesealing of channels with meltable material. In one embodiment, thedevice comprises a meltable material disposed within a substrate andassociated with a heating element.

In one embodiment, the present invention contemplates a methodcomprising: a) providing a device having a meltable material disposedwithin a substrate and associated with a heating element; and b) heatingsaid meltable material with said heating element such that said meltablematerial at least partially liquifies and such that said substrate isnot damaged. The method may further comprise c) allowing said liquifiedmeltable material to cool. While the present invention is not limited bythe size of the channel, in one embodiment said substrate furthercomprises a microdroplet channel disposed in said substrate, saidmeltable material is disposed within said microdroplet channel.

In another embodiment, the present invention contemplates a method forrestricting fluid flow in a channel comprising a) providing a devicecomprising: i) a meltable material disposed within a substrate, saidmeltable material associated with a heating element; and ii) a diaphragmpositioned such that, when extended, it touches said meltable material;b) extending said diaphragm such that it touches said meltable material;and c) heating said meltable material with said heating element suchthat said meltable material at least partially liquifies and such thatsaid substrate is not damaged. In one embodiment the method furthercomprises d) allowing said meltable material to cool. While the presentinvention is not limited by the size of the channel, in one embodiment,the substrate further comprises a microdroplet channel disposed in saidsubstrate, said meltable material disposed within said microdropletchannel.

The present invention also contemplates a method for restricting fluidflow in a channel, comprising: a) providing: i) a main channel connectedto a side channel and disposed within a substrate, ii) meltable materialdisposed within said side channel and associated with a heating element,and iii) a movement means connected to said side channel such thatapplication of said movement means induces said meltable material toflow from said side channel into said main channel; b) heating saidmeltable material such that said meltable material at least partiallyliquifies; and c) applying said movement means such that said liquifiedmeltable material flows from said side channel into said main channel.While the present invention is not limited by the movement means, in oneembodiment the movement means is forced air. In one embodiment themethod further comprises d) allowing said meltable material to cool.While the present invention is not limited by the size of the charnel,in one embodiment, the main channel and the side channel aremicrodroplet channels.

While the present invention is not limited by the nature of thesubstrate, in one embodiment the substrate comprises silicon or glass.Likewise, the present invention is not limited by the composition of themeltable material. In one embodiment, the meltable material comprisessolder. In a preferred embodiment, the solder comprises 40:60 Sn:Pb. Inother embodiments, the meltable material is selected from a groupconsisting of plastic, polymer and wax. Likewise, the present inventionis not limited by the placement of the meltable material in thesubstrate. In another embodiment, the meltable material is placedadjacent to a channel, while in another embodiment it is placed near thejunction of more than one channel.

Definitions

The following definitions are provided for the terms used herein:

“Biological reactions” means reactions involving biomolecules such asenzymes (e.g., polymerases, nucleases, etc.) and nucleic acids (both RNAand DNA).Biological samples are those containing biomolecules, suchproteins, lipids, nucleic acids. The sample may be from a microorganism(e.g., bacterial culture) or from an animal, including humans (e.g.blood, urine, etc.). Alternatively, the sample may have been subject topurification (e.g. extraction) or other treatment. Biological reactionsrequire some degree of biocompatability with the device. That is to say,the reactions ideally should not be substantially inhibited by thecharacteristics or nature of the device components.

“Chemical reactions” means reactions involving chemical reactants, suchas inorganic compounds.

“Channels” are pathways (whether straight, curved, single, multiple, ina network, etc.) through a medium (e.g., silicon) that allow formovement of liquids and gasses. Channels thus can connect othercomponents, i.e., keep components “in communication” and moreparticularly, “in fluidic communication” and still more particularly,“in liquid communication.” Such components include, but are not limitedto, gas-intake channels and gas vents.

“Microdroplet transport channels” are channels configured (in microns)so as to accommodate “microdroplets.” While it is not intended that thepresent invention be limited by precise dimensions of the channels orprecise volumes for microdroplets, illustrative ranges for channels andmicrodroplets are as follows: the channels can be between 0.5 and 50 μmin depth (preferably between 5 and 20 μm) and between 20 and 1000 μm inwidth (preferably 500 μm), and the volume of the microdroplets can range(calculated from their lengths) between approximately 0.01 and 100nanoliters (more typically between ten and fifty).

“Conveying” means “causing to be moved through” as in the case where amicrodroplet is conveyed through a transport channel to a particularpoint, such as a reaction region. Conveying can be accomplished viaflow-directing means.

“Flow-directing means” is any means by which movement of liquid (e.g. amicrodroplet) in a particular direction is achieved. A variety offlow-directing means are contemplated, including but not limited topumps such as a “bubble pump” described below. A preferred directingmeans employs a surface-tension-gradient mechanism in which discretedroplets are differentially heated and propelled through etchedchannels. For continuous flow of liquids, pumps (both external andinternal) are contemplated.

A “bubble pump” is one embodiment of a flow-directing means, liquid isintroduced into a channel, said channel comprising one or moreelectrodes positioned such that they will be in contact with a liquidsample placed in said channel. Two electrodes can be employed and apotential can be applied between the two electrodes. At both ends of theelectrodes, hydrolysis takes place and a bubble is generated. The gasbubble continues to grow as the electrodes continue pumping electricalcharges to the fluid. The expanded bubble creates a pressuredifferential between the two sides of the liquid drop which eventuallyis large enough to push the liquid forward and move it through thepolymer channel.

When coupled with the capillary valve, a bubble pump can actuate acertain quantity of fluidic samples along the channel. The capillaryvalve is essentially a narrow section of a channel. In operation, thefluidic sample is first injected in the inlet reservoir. As soon as thefluid is loaded, it moves in the channel by capillary force. The fluidthen passes the narrow section of the channel but stops at the edgewhere the channel widens again. After the fluidic sample is loaded, apotential is applied between two electrodes. At both ends of theelectrodes, hydrolysis occurs and bubble is generated. The bubble keepson growing as the electrodes continue pumping electrical charges to thefluid. The expanding bubble then creates a pressure differential betweenthe two sides of the liquid drop, which eventually large enough to pushthe liquid forward.

The combination of bubble pump and capillary valve does not require anymoving parts and is easy to fabricate. In addition, the device producesa well-controlled fluid motion, which depends on the bubble pressure.The bubble pressure is controlled by the amount of charges pumped by theelectrodes. Furthermore, the power consumption of the device is minimal.

“Hydrophilicity-enhancing compounds” are those compounds or preparationsthat enhance the hydrophilicity of a component, such as thehydrophilicity of a transport channel. The definition is functional,rather than structural. For example, Rain-X™ anti-fog is a commerciallyavailable reagent containing glycols and siloxanes in ethyl alcohol.However, the fact that it renders a glass or silicon surface morehydrophilic is more important than the reagent's particular formula.

“Hydrophobic reagents” are used to make “hydrophobic coatings” inchannels. It is not intended that the present invention be limited toparticular hydrophobic reagents. In one embodiment, the presentinvention contemplates hydrophobic polymer molecules that can be graftedchmically to the silicon oxide surface. Such polymer molecules include,but are not limited to, polydimethylsiloxane. In another embodiment, thepresent invention contemplates the use of silanes to make hydrophobiccoatings, including but not limited to halogenated silanes andalkylsilanes. In this regard, it is not intended that the presentinvention be limited to particular silanes; the selection of the silaneis only limited in a functional sense, i.e. that it render the surfacehydrophobic.

In one embodiment, n-octadecyltrichlorosilane (OTS) is used as ahydrophobic reagent. In another embodiment,octadecyldimethylchlorosilane is employed. In yet another embodiment,the present invention contemplates 1H,1H, 2H,2H-perfluorodecyltricholorosilane (FDTS, C₁₀H₄F₁₇SiCl₃) as a hydrophobicreagent. In still other embodiments, fluoroalkyl-, aminoalkyl-, phenyl-,vinyl-, bis silyl ethane- and 3-methacryloxypropyltrimethoxysilane(MAOP) are contemplated as hydrophobic reagents. Such reagents (ormixtures thereof) are useful for making hydrophobic coatings, and morepreferably, useful for making regions of a channel hydrophobic (asdistinct from coating the entire channel).

It is not intended that the present invention be limited to particulardimensions for the hydrophobic regions of the present invention. While avariety of dimensions are possible, it is generally preferred that theregions have a width of between approximately 10 and 1000 μm (or greaterif desired), and more preferably between approximately 100 and 500 μm.

A surface (such as a channel surface) is “hydrophobic” when it displaysadvancing contact angles for water greater than approximately seventydegrees. In one embodiment, the treated channel surfaces of the presentinvention display advancing contact angles for water betweenapproximately ninety (90) and approximately one hundred and thirty (130)degrees. In another embodiment, the treated microchannels have regionsdisplaying advancing contact angles for water greater than approximatelyone hundred and thirty (130) degrees.

A “liquid-abutting hydrophobic region” is a hydrophobic region within achannel which has caused liquid (e.g. aqueous liquid) to stop or beblocked from further movement down the channel, said stopping orblocking being due to the hydrophobicity of the region, said stopped orblocked liquid positioned immediately adjacent to said hydrophobicregion.

“Initiating a reaction” means causing a reaction to take place.Reactions can be initiated by any means (e.g. heat, wavelengths oflight, addition of a catalyst, etc.)

“Liquid barrier” or “moisture barrier” is any structure or treatmentprocess on existing structures that prevents short circuits and/ordamage to electronic elements (e.g., prevents the destruction of thealuminum heating elements). In one embodiment of the present invention,the liquid barrier comprises a first silicon oxide layer, a siliconnitride layer, and a second silicon oxide layer.

“Merging” is distinct from “mixing.” When a first and secondmicrodroplet is merged to create a merged microdroplet, the liquid mayor may not be mixed. Moreover, the degree of mixing in a mergedmicrodroplet can be enhanced by a variety of techniques contemplated bythe present invention, including by not limited to reversing the flowdirection of the merged microdroplet.

“Nucleic Acid Amplification” involves increasing the concentration ofnucleic acid, and in particular, the concentration of a particular pieceof nucleic acid. A preferred technique is known as the “polymerase chainreaction.” Mullis et at., U.S. Pat. Nos. 4,683,195 and 4,683,202, herebyincorporated by reference, describe a method for increasing theconcentration of a segment of target sequence in a mixture of genomicDNA without cloning or purification. This process for amplifying thetarget sequence consists of introducing a molar excess of twooligonucleotide primers to the DNA mixture containing the desired targetsequence. The two primers are complementary to their respective strandsof the double-stranded sequence. The mixture is denatured and thenallowed to hybridize. Following hybridization, the primers are extendedwith polymerase so as to form complementary strands. The steps ofdenaturation, hybridization, and polymerase extension can be repeated asoften as needed to obtain are relatively high concentration of a segmentof the desired target sequence. The length of the segment of the desiredtarget sequence is determined by the relative positions of the primerswith respect to each other, and therefore, this length is a controllableparameter. By virtue of the repeating aspect of the process, the methodis referred to by the inventors as the “Polymerase Chain Reaction”(hereinafter PCR). Because the desired segment of the target sequencebecome the dominant sequences (in terms of concentration) in themixture, they are said to be “PCR-amplified.”

“Substrate” as used herein refers to a material capable of containingchannels and microdroplet transport channels. Examples include, but arenot limited to, silicon and glass.

“Meltable material” as used herein refers to a material that is at leastsemi-solid (and preferably completely solid) at ambient temperature,will liquify when heated to temperatures above ambient temperature, andwill at least partially resolidify when cooled. Preferably, meltablematerial at least partially liquifies at a temperature such that thesubstrate is undamaged. That is to say, at the temperature the meltablematerial liquifies, the substrate and other metals in the substrate doesnot liquify (readily tested as set forth in Example 6) and does notchange its properties. By “changing properties” it is meant that thesubstrate or metal maintains it structural integrity, does not changeits conductivity and does not liquify. Thus, the characteristic of beingmeltable is not necessarily associated with a particular melting point.Examples include, but are not limited to, solder, wax, polymer andplastic.

“Solder” as used herein refers to a metal or alloy that is a meltablematerial. Preferably, the solder is a lower temperature solder, such asset forth in U.S. Pat. No. 4,967,950, herein incorporated by reference.“Lower temperature solder” means a eutectic alloy. While the presentinvention is not limited to a specific solder, one preferred soldercomposition for the paste is a 63:37 eutectic alloy of tin:lead. Anothercompatible solder is a 90% metal composition having a 63:35:2 eutecticalloy of tin:lead:silver. Other desired solder compositions such aseutectic Pb:Sn, Pb:In, Pb:In:Sn etc.

“Heating element” as used herein refers to an element that is capable ofat least partially liquify a meltable material. A meltable material is“associated with” a heating element when it is in proximity to theheating element such that the heating element can at least partiallymelt the meltable material. The proximity necessary will depend on themelting characteristics of the meltable material as well as the heatingcapacity of the heating element. The heating element may or may not beencompassed within the same substrate as the meltable material.

“Diaphragm” as used herein refers to an element capable of beingmanipulated such that it can at least partially block the passage offluid in a channel in one position (extended) and permit the flow offluid in a channel in another position. An “actuating force” is a forcethat is capable of extending a diaphragm. A “valve seat” is an elementdesigned to accept a portion of the diaphragm when extended. A “movementmeans” is a means capable of moving liquified meltable material (e.g.,force air, magnetic field, etc.).

A “source of liquid microdroplets” is a liquid source from whichmicrodroplets can be made. Such sources include, but are not limited to,continuous streams of liquid as well as static sources (such as liquidin a reservoir). In a preferred embodiment, the source of liquidmicrodroplets comprises liquid in a microchannel from whichmicrodroplets of a discrete size are split off.

DESCRIPTION OF THE DRAWINGS

FIG. 1 is a schematic of an integrated analysis system of the presentinvention.

FIG. 2 shows a two-part approach to construction of a silicon device ofthe present invention.

FIG. 3A presents a schematic of one embodiment of a device wherein thefront of the liquid moves by (but does not enter) a gas-intake pathway(50) that is in fluidic communication with the channel.

FIG. 3B presents a schematic of one embodiment of the device wherein gasis introduced to split off a microdroplet.

FIG. 4A shows a schematic of one embodiment of a device of the presentinvention to split, move and stop microdroplets using internal gaspressure generation.

FIG. 4B shows a schematic of another embodiment of a device of thepresent invention to split, move and stop microdroplets using internalgas pressure generation.

FIG. 5 is a schematic showing the principle of thermally-induced liquidmicrodroplet motion in a closed channel.

FIG. 6A shows a selected frame of a videotape wherein two microdropletsare at their starting locations in the branches of the Y-channel.

FIG. 6B shows movement by heating the left interface of bothmicrodroplets.

FIG. 6C shows the microdroplets at the intersection.

FIG. 6D shows the merging of the microdroplets to form the combinedmicrodroplet. The open arrowheads in the figure indicate the rearmeniscus and the filled arrowheads the leading meniscus for eachmicrodroplet.

FIG. 7A is a photomicrograph of inlay-process heater elements on thesurface of a silicon wafer.

FIG. 7B is a scanning electron micrograph (SEM) of an inlay-processheater wire in cross section (the arrows indicate the depositedaluminum, silicon dioxide, and silicon nitride layers).

FIG. 7C is a SEM of a channel formed on glass using a wet-etch process,shown in cross section with the etched face of the wafer immediatelyadjacent to the intersection of two channels.

FIG. 8A is a schematic of one embodiment of the device of the presentinvention wherein the device comprises a glass top bonded to a siliconsubstrate.

FIG. 8B is a schematic showing one embodiment of the fabrication stepsfor fabrication of components in silicon.

FIG. 8C is a schematic showing one embodiment of the fabrication stepsfor fabrication of components in glass.

FIG. 9A is a photomicrograph of polyacrylamide gel electrophoresis in awide etched-glass channel.

FIG. 9B is a photomicrograph of a set of four doped-diffusion dioderadiation detector elements fabricated on a silicon wafer.

FIG. 9C is an oscilloscope trace of output from the radiation detectorshowing individual decay events from ³²P-labeled DNA.

FIG. 10 is a photo of gel electrophoresis of PCR reactions whereinpotentially inhibiting components were added directly to the PCR.

FIG. 11 is one embodiment of a test device for the present invention.

FIGS. 12A-J are schematics for an embodiment for manufacturing asealable valve of the present invention.

FIG. 13 is a schematic of one embodiment for the layout of the movablesealing means of the present invention.

FIG. 14 is a photograph showing water droplets separated by lines ofhydrophobic and hydrophilic regions patterned according to the methodsof the present invention.

FIG. 15A is photograph showing simple patterning according to themethods of the present invention to create multiple droplets.

FIG. 15B is photograph showing simple patterning according to themethods of the present invention to create multiple droplets.

FIG. 15C is photograph showing simple patterning according to themethods of the present invention to create multiple droplets.

FIG. 16A presents a photograph of one embodiment of the device of thepresent invention utilizing a heater.

FIG. 16B presents a photograph of one embodiment of the device of thepresent invention utilizing a heater.

FIG. 16C presents a photograph of one embodiment of the device of thepresent invention utilizing a heater.

FIG. 16D presents a photograph of one embodiment of the device of thepresent invention utilizing a heater.

FIG. 16E presents a photograph of one embodiment of the device of thepresent invention utilizing a heater.

FIG. 16F presents a schematic of one embodiment of the device of thepresent invention utilizing a heater.

FIG. 16G presents a schematic of one embodiment of the device of thepresent invention utilizing a heater.

FIG. 16H presents a schematic of one embodiment of the device of thepresent invention utilizing a heater.

FIG. 16I presents a schematic of one embodiment of the device of thepresent invention utilizing a heater.

FIG. 16J presents a schematic of one embodiment of the device of thepresent invention utilizing a heater.

DESCRIPTION OF THE INVENTION

The present invention relates to microfabrication and biologicalreactions in microfabricated devices, and in particular, movement andmixing of biological samples in microdroplets through microchannels. Thedescription of the invention involves I) the design of microscaledevices (comprising microdroplet transport channels, reaction chambers,electrophoresis ports, and radiation detectors) using silicon and glasssubstrates, II) the creation (or definition) of microdroplets having adiscrete size, III) movement of discrete micro droplets using asurface-tension-gradient mechanism in which discrete microdroplets aredifferentially heated and propelled through etched channels, IV) flowcontrol with sealed valves, and V) mixing of biological samples forreactions.

I. Design Of MicroScale Devices

Although there are many formats, materials, and size scales forconstructing integrated fluidic systems, the present inventioncontemplates silicon microfabricated devices as a cost-effectivesolution. Silicon is the material used for the construction of computingmicroprocessors and its fabrication technologies have developed at anunprecedented pace over the past 30 years. While this technology wasinitially applied to making microelectronic devices, the same techniquesare currently being used for micromechanical systems.

Continuous flow liquid transport has been described using a microfluidicdevice developed with silicon. See J. Pfahler et al., Sensors andActuators, A21-A23 (1990), pp. 431-434. Pumps have also been described,using external forces to create flow, based on micromachining ofsilicon. See H. T. G. Van Lintel et al., Sensors and Actuators15:153-167 (1988). By contrast, the present invention employs discretedroplet transport in silicon (i.e., in contrast to continuous flow)using internal forces (i.e., in contrast to the use of external forcescreated by pumps).

As a mechanical building material, silicon has well-known fabricationcharacteristics. The economic attraction of silicon devices is thattheir associated micromachining technologies are, essentially,photographic reproduction techniques. In these processes, transparenttemplates or masks containing opaque designs are used to photodefineobjects on the surface of the silicon substrate. The patterns on thetemplates are generated with computer-aided design programs and candelineate structures with line-widths of less than one micron. Once atemplate is generated, it can be used almost indefinitely to produceidentical replicate structures. Consequently, even extremely complexmicromachines can be reproduced in mass quantities and at lowincremental unit cost—provided that all of the components are compatiblewith the silicon micromachining process. While other substrates, such asglass or quartz, can use photolithographic methods to constructmicrofabricated analysis devices, only silicon gives the added advantageof allowing a large variety of electronic components to be fabricatedwithin the same structure.

In one embodiment, the present invention contemplates siliconmicromachined components in an integrated analysis system, including theelements identified schematically in FIG. 1. In this proposed format,sample and reagent are injected into the device through entry ports (A)and they are transported as discrete droplets through channels (B) to areaction chamber, such as a thermally controlled reactor where mixingand reactions (e.g., restriction enzyme digestion or nucleic acidamplification) occur (C). The biochemical products are then moved by thesame method to an electrophoresis module (D) where migration data iscollected by a detector (E) and transmitted to a recording instrument(not shown). Importantly, the fluidic and electronic components aredesigned to be fully compatible in function and construction with thebiological reactions and reagents.

In silicon micromachining, a simple technique to form closed channelsinvolves etching an open trough on the surface of a substrate and thenbonding a second, unetched substrate over the open channel. There are awide variety of isotropic and anisotropic etch reagents, either liquidor gaseous, that can produce channels with well-defined side walls anduniform etch depths. Since the paths of the channels are defined by thephoto-process mask, the complexity of channel patterns on the device isvirtually unlimited. Controlled etching can also produce sample entryholes that pass completely through the substrate, resulting in entryports on the outside surface of the device connected to channelstructures.

FIG. 2 shows a two-part approach to construction. Microchannels (100)are made in the silicon substrate (200) and the structure is bonded to aglass substrate (300). The two-part channel construction techniquerequires alignment and bonding processes but is amenable to a variety ofsubstrates and channel profiles. In other words, for manufacturingpurposes, the two-part approach allows for customizing one piece (i.e.,the silicon with channels and reaction formats) and bonding with astandardized (non-customized) second piece, e.g., containing standardelectrical pads (400).

II. The Creation Of MicroDroplets

The present invention contemplates methods, compositions and devices forthe creation of microdroplets of discrete (i.e. controlled andpredetermined) size. The present invention contemplates the use ofselective hydrophobic coatings to develop a liquid-sample injection andmotion system that does not require the use of valves. In oneembodiment, the present invention contemplates a method of lift-off topattern hydrophobic and hydrophilic regions on glass, quartz and siliconsubstrates, involving i) the deposition of a hydrophobic reagent (suchas a self-assembled monolayer film of OTS) on a silicon oxide surfacepattered by a metal layer and ii) subsequent removal of the metal togive hydrophobic patterns. Other substrates such as plastics can also beused after depositing a think film of silicon oxide or spin-on-glass.

Previous work in patterning hydrophobic surfaces have been done byphotocleaving of such monolayer films. The photocleaving procedure usesDeep-UV exposure to make the molecules of the monolayer hydrophilic. Bycontrast, the present invention contemplates a method which eliminatesthe use of high-power UV source; rather the preferred method of thepresent invention uses simple microfabrication procedures.

Following the proper hydrophobic patterning of the surface (e.g. thesurface of a microdroplet transport channel), the present inventioncontemplates the placement of a patterned etched glass cap over thepattern on a flat surface. The hydrophobic/hydrophilic channels thusformed can then be used to move precise nanoliter-volume liquid samples.

FIGS. 3A and 3B show a schematic of one embodiment of a device to splita nonoliter-volume liquid sample and move it using external air, saiddevice having a plurality of hydrophobic regions. Looking at FIG. 3A,liquid (shown as solid black) placed at the inlet (20) is drawn in bysurface forces and stops in the channel at the liquid-abuttinghydrophobic region (40), with overflow handled by an overflow channeland overflow outlet (30). In the embodiment shown in FIG. 3A, the frontof the liquid moves by (but does not enter) a gas-intake pathway (50)that is in fluidic communication with the channel; the liquid-abuttinghydrophobic region (40) causes the liquid to move to a definitelocation. Gas from a gas source (e.g. air from an external air sourceand/or pump) can then be injected (FIG. 3B, lower arrow) to split amicrodroplet of length “L”. The volume of the microdroplet split-off(60) is pre-determined and depends on the length “L” and the channelcross-section. To prevent the the pressure of the gas (e.g. air) fromacting towards the inlet side, the inlet (20) and overflow ports (30)can be blocked or may be loaded with excess water to increase theresistance to flow.

The patterened surfaces can also be used to control the motion of thedrop. By placing a hydrophobic gas vent (70) further down the channel,one can stop the liquid microdroplet (60) after moving beyond the vent(70). As the drop (60) passes the vent (70), the air will go out throughthe vent (70) and will not push the drop further.

One can start moving the drop (60) again by blocking the vent (70). Byusing a combination of hydrophobic air pressure lines (not shown),hydrophobic vents and strategic opening and/or closing of vents, one canmove the liquid drop back and forth for mixing or move it to preciselocations in a channel network to perform operations such as heating,reaction and/or separations.

In addition to using external air, one can also use internally generatedair pressure to split and move drops. FIGS. 4A and 4B present schematicsof one embodiment of a device (10) of the present invention to split(e.g. define), move and stop microdroplets using internal gas (e.g. air)pressure generation, said device having a plurality of hydrophobicregions. Looking at FIG. 4A, liquid (shown as solid black) placed at theinlet (120) is drawn in by surface forces and stops in the channel atthe liquid-abutting hydrophobic region (140), with overflow handled byan overflow channel and overflow outlet (130). In the embodiment shownin FIG. 4A, the front of the liquid moves by (but does not enter) agas-intake pathway (150) that is in fluidic communication with thechannel. By heating air trapped inside chambers (180) that are influidic communication with the microdroplet transport channel via thegas-intake pathway (150), an increased pressure can be generated. Themagnitude of the pressure increase inside a chamber of volume V isrelated to the increase in temperature and can be estimated by the IdealGas relation:

Increasing the temperature of the gas (e.g. air) will cause the pressureinside the chamber to rise until the pressure is high enough to splitoff a drop (160) and move it beyond the liquid-abutting hydrophobicregion (140). In order to avoid the problem of the expanded air heatingup the liquid, the chamber may be placed at a distance from thetransport channel. Moreover, having the heaters suspended inside the airchamber or placing them on a thin insulation membrane will not onlyavoid cross-talk, but will involve a minimal power consuption.

The compositions and methods are suitable for devices having a varietyof designs and dimensions, including, but not limited to, devices withchamber volumes from 0.24 mm¹ to 0.8 mm³ for channel dimensions of 40 μmby 500 μm. Drop splitting and motion is seen with 1-3 seconds usingvoltages between 4.5 volts to 7.5 volts (the resistance of the heatersvaried between 9.5 ohms to 11 ohms). The size of the drop split isbetween approximately 25 and approximately 50 nanoliters, depending onthe value “L” used for the channel design. Keeping the heaters actuatedkeeps the microdroplet moving almost to the end of the channel (adistance of around 12.5 mm); the time taken depends on the voltageapplied to the heater and the volume of the chamber. Initiation of dropmotion is seen sooner for the operation of devices with smallerchambers. While an understanding of precise mechanisms is not needed forthe successful practice of the present invention, it is believed thatwith smaller chamber, the volume is smaller and higher values ofpressure are achieved more quickly. The maximum temperatures reachednear the heater are approximately 70° C. measured by the RTD.

III. Movement Of Discrete MicroDroplets

The present invention describes the controlled movement of liquidsamples in discrete droplets in silicon. Discrete droplet transportinvolves a system using enclosed channels or tubes to transport theliquid to the desired locations (FIG. 1, B). Within the channels,discrete liquid reagent microdroplets can be injected, measured, andmoved between the biochemical analysis components. Discrete dropletmovement has three advantages. First, each sample droplet is separatedfrom all others so that the risk of contamination is reduced. Second, ina uniform channel, the volume of each sample can be determined by merelymeasuring the droplet length. Third, the motion of these droplets can beaccomplished with simple heating (i.e., using internal forces and nomoving parts). Movement is performed using thermal gradients to changethe interfacial tension at the front or back of the droplets and, thus,generate pressure differences across the droplet (FIG. 5). For example,a droplet in a hydrophilic channel can be propelled forward by heatingthe back interface. The local increase in temperature reduces thesurface tension on the back surface of the droplet and, therefore,decreases the interfacial pressure difference. The decreased pressuredifference corresponds to an increase in the local internal pressure onthat end of the droplet (P₁ increases). The two droplet interfaces areno longer in equilibrium, with P₁ greater than P₂, and the pressuredifference propels the droplet forward.

That is to say, forward motion can be maintained by continuing to heatthe droplet at the rear surface with successive heaters along thechannel, while heating the front surface can be used to reverse themotion of the droplet. Applying a voltage to the wire beneath thechannel generates heat under the edge of the droplet. Heating the leftinterface increases the internal pressure on that end of the droplet andforces the entire droplet to the right. The pressure on the interior ofthe droplet can be calculated knowing the atmospheric pressure,P_(atnp), the surface tension, σ, and the dimensions of the channel. Fora circular cross-section, the interior pressure, P_(i), is given byP_(i)=P_(atm)−(4σ cos θ)/d where d is the diameter of the channel and θis the contact angle. Since a is a function of temperature(σ=σ_(n)(1−bT) where σ_(o) and b are positive constants and T is thetemperature), increasing the temperature on the left end of the dropletdecreases the surface tension and, therefore, increases the internalpressure on that end. The pressure difference between the two ends thenpushes the droplet towards the direction of lower pressure (i.e.,towards the right). The aqueous droplet shown is in a hydrophilicchannel (0<θ<90); for a hydrophobic channel (90<θ<180), heating theright edge would make the droplet move to the right.

Contact angle hysteresis (the contact angle on the advancing edge of thedroplet is larger than the contact angle on the retreating edge)requires a minimum temperature difference before movement will occur.The velocity of the droplet after motion begins can be approximatedusing the equation v=AEPd²/32 μL where AEP is the pressure difference, μis the viscosity of the solution, and L is the length of the droplet.The present invention contemplates temperature differences of greaterthan thirty (30) degrees Centigrade to create movement. Experimentsusing temperature sensors arrayed along the entire channel indicate thata differential of approximately 40° C. across the droplet is sufficientto provide motion. In these experiments, the channel cross-section was20 μm×500 μm, and the volume of each of these droplets can be calculatedfrom their lengths and is approximately 100 nanoliters for a 1 cm longdroplet.

IV. Flow Control with Sealed Valves

The present invention contemplates the use of sealed valves to controlfluid flow. While the present invention is not limited to a particularsealing method, in one embodiment, an actuating force pushes a diaphragmagainst a valve seat to restrict fluid flow and the diaphragm is thensealed to the valve seat. In such an embodiment, the solder pads areassociated with a heating element that can melt the solder. Thisliquified solder flows over areas of the valve seat and diaphragm tocover contamination, cracks and crooks between the diaphragm and valveseat. With the actuating force still holding the diaphragm andvalve-seat together, the heating element is turned off to allow thesolder to cool and re-solidify. Upon solidification, the actuating forcecan be released and the valve is sealed. To open the valve again, thesolder can be liquified without applying an actuation force.

In a preferred embodiment, the valve is designed such that solder padsare placed on the diaphragm or valve seat. While the present inventionis not limited to a precise method of placing these solder pads, it isspecifically contemplated that they can be electroplated.

V. Mixing Biological Samples In Reactions

Droplet motion (described generally above) is contemplated as one stepin a pathway. The other steps typically involve sample mixing and acontrolled reaction. For example, the integral heaters arrayed along theentire surface of the channel used for droplet motion also allow for aregion of a channel to be used as a thermal reaction chamber. For samplemixing prior to the reaction, a Y-channel device is contemplated (FIG.6A). In such a device, a first droplet containing a first sample (e.g.,nucleic acid) is moved along one channel of the Y-channel device, and asecond droplet containing a second sample (e.g., a restriction digestenzyme in digestion buffer) is moved along the other channel of theY-channel device (FIGS. 6B and 6C)

Following sample merging (FIG. 6D), there is the concern that thecombined samples have not been properly mixed. That is to say, if twosimilar microdroplets enter the single channel in laminar flow at thesame flow rate, they will form an axially uniform droplet but will notbe mixed width-wise. Width-mixing can be accomplished in a number ofways.

First, there is simple diffusion, although, for large DNA molecules, thecharacteristic time for this mixing could be on the order of severalhours or more. Circulation patterns generated inside the droplets duringmovement and heating significantly reduce this time. In this regard, thepresent invention contemplates maintaining the mixture as a heatedmixture (e.g., maintaining the temperature at 65° C. for 10 minutes)using the integral heaters and temperature sensors.

Second, the present invention contemplates mixing by reversing the flowdirection of the mixture over a relatively short distance in thechannel. While a variety of reverse flow approaches are possible, one ortwo direction changes over a distance comprising approximately twodroplet lengths has been found to be adequate.

Finally, there is the mixing approach wherein the mixture is movedagainst or over physical obstacles. For example, the mixture can beeither “crashed” back against merge point of the Y-channel or simplymoved over deliberate imperfections in the channel (i.e., “rollercoaster” mixing).

Successful mixing, of course, can be confirmed by characterization ofthe product(s) from the reaction. Where product is detected, mixing hasbeen at least partially successful. The present invention contemplates,in one embodiment, using electrophoresis to confirm product formation.

DESCRIPTION OF PREFERRED EMBODIMENTS

The description of the preferred embodiments involves: I)microfabrication techniques for manufacture of silicon-based devices;II) channel treatment for optimum flow and reproducibility; III) channeltreatment for fabricating hydrophobic regions, and IV) component design(particularly the electrophoresis module and the radiation detectors).

I. Microfabrication Of Silicon-Based Devices

As noted previously, silicon has well-known fabrication characteristicsand associated photographic reproduction techniques. The principalmodern method for fabricating semiconductor integrated circuits is theso-called planar process. The planar process relies on the uniquecharacteristics of silicon and comprises a complex sequence ofmanufacturing steps involving deposition, oxidation, photolithography,diffusion and/or ion implantation, and metallization, to fabricate a“layered” integrated circuit device in a silicon substrate. See e.g., W.Miller, U.S. Pat. No. 5,091,328, hereby incorporated by reference.

For example, oxidation of a crystalline silicon substrate results in theformation of a layer of silicon dioxide on the substrate surface.Photolithography can then be used to selectively pattern and etch thesilicon dioxide layer to expose a portion of the underlying substrate.These openings in the silicon dioxide layer allow for the introduction(“doping”) of ions (“dopant”) into defined areas of the underlyingsilicon. The silicon dioxide acts as a mask; that is, doping only occurswhere there are openings. Careful control of the doping process and ofthe type of dopant allows for the creation of localized areas ofdifferent electrical resistivity in the silicon. The particularplacement of acceptor ion-doped (positive free hole, “p”) regions anddonor ion-doped (negative free electron, “n”) regions in large partdefines the interrelated design of the transistors, resistors,capacitors and other circuit elements on the silicon wafer. Electricalinterconnection and contact to the various p or n regions that make upthe integrated circuit is made by a deposition of a thin film ofconductive material, usually aluminum or polysilicon, thereby finalizingthe design of the integrated circuit.

Of course, the particular fabrication process and sequence used willdepend on the desired characteristics of the device. Today, one canchoose from among a wide variety of devices and circuits to implement adesired digital or analog logic feature.

In a preferred embodiment, channels were prepared on 500 μm thick glasswafers (Dow Corning 7740) using standard aqueous-based etch procedures.The initial glass surface was cleaned and received two layers ofelectron beam evaporated metal (20 nm chromium followed by 50 nm gold).Photoresist Microposit 1813 (Shipley Co.) was applied 4000 rpm, 30seconds; patterned using glass mask 1 and developed. The metal layerswere etched in chromium etchant (Cr-14, Cyantek Inc.) and gold etchant(Gold Etchant TFA, Transene Co.) until the pattern was clearly visibleon the glass surface. The accessible glass was then etched in a solutionof hydrofluoric acid and water (1:1, v/v). Etch rates were estimatedusing test wafers, with the final etch typically giving channel depthsof 20 to 30 μm. For each wafer, the depth of the finished channel wasdetermined using a surface profilometer. The final stripping (PRS-2000,J. T. Baker) removed both the remaining photoresist material and theoverlying metal.

In one embodiment, channels etched on glass in the above-describedmanner, were bonded to the heater-element wafer in a two-partconstruction approach using optical adhesive (SK-9 Lens Bond, SumersLaboratories, Fort Washington, Pa.). The bond was cured under anultraviolet light source (365 nm) for 12 to 24 hours.

Initial device design by the present inventors involved single layers ofsilicon. However, experience showed these to be inadequate to preventshort circuiting due to (necessary) liquid microdroplets within thechannels (see experiments described below). The preferred designinvolves a triple layer of oxides. Such a preferred device capable ofmoving and mixing nanoliter droplets was constructed by bonding a planarsilicon substrate to channels etched in a glass cover. A series of metalheaters was inlaid on the silicon substrate as two parallel lanesmerging into a single lane (a “Y”-shape) (FIG. 7A). The heating elementswere formed by first coating the wafer with a 1.0 μm layer of thermalsilicon dioxide Next, 0.35 μm deep, 5 μm wide grooves were reactive-ionetched (RIE) into the silicon dioxide following the pattern set in anoverlying photoresist. Aluminum was deposited (0.35 μm) across theentire wafer using electron beam evaporation and the metal layer was“lifted-off” from all surfaces having intact photoresist using astripping solution. The metal inlay process gives a relatively planarsurface and provides a uniform base for deposition of asolution-impermeable barrier layer. The barrier layer is made by asequence of three plasma-enhanced chemical vapor depositions (PECVD):1.0 μm silicon oxide (SiO_(x)), 0.25 μm silicon nitride (Si_(x)N_(y)),and 1.0 μm silicon oxide (SiO_(x)) (FIG. 7B). Some heating elements werealso used as resistive temperature sensors.

Heater elements were fabricated as follows. Silicon wafer (p-type,18-22½-cm, <100>, boron concentration Å 10¹⁵ cm³) was used as asubstrate for growth of SiO₂ thermal oxide (1 μm); photoresist(AZ-5214-E, Hoescht-Celanese) was applied and spun at 3000 rpm, 30seconds. The resist was patterned (metal 1) and developed. Reactive ionetch (RIE, PlasmaTherm, Inc.) was performed to 0.35 μm depth into theSiO₂ layer at the following conditions: CHF₃, 15 sccm (standard cubiccentimeters per minute); CF₄, 15 sccm; 4 mTorr; DC bias voltage of 200V,100 W, 20 minutes. The etch depth was measured by profilometer and 0.35μm metallic aluminum was electron beam deposited. The resist andoverlying metal was lifted off by development using Microposit 1112Aremover in solution (Shipley Co.). The barrier layers consist ofsequentially deposited 1 μm SiO_(x), 0.25 μm Si_(x)N_(y), and 1 μm SiOXusing plasma-enhanced chemical vapor deposition (PECVD). RIE was used toetch contact holes to the metal layer using a second mask (CHF₃, 15sccm; CF₄, 15 sccm; 4 mTorr; and DC bias voltage of 200V, 100 W, 120minutes).

As shown in FIGS. 7A, 7B, and 7C the elements are arrayed as twoparallel lanes, each 500 μm wide, merging into one lane. The individualheaters consist of paired aluminum wires (5 μm) winding across the 500μm wide region. The broad metal areas on either side of the elements arebonding locations for connection to external circuitry. The width of thealuminum element is 5 μm. The channel in FIG. 7C has identical width anddesign configurations as the heating element lanes in FIG. 7A, and isuniformly etched 500 μm wide and approximately 20 μm deep.

The heating-element wafer was bonded to a glass wafer containing etchedchannels with the same “Y” format. An aqueous chemical etch ofconcentrated hydrofluoric acid was used to produce channels with definedside walls and uniform depth. The etched channels are defined by achromium/gold mask and are 500 μm wide and approximately 20 μm deep. Thecomplementary silicon heater and glass channel wafers were aligned andthen bonded with adhesive to form the finished device.

Each heating element used as a temperature sensor is preferably firstcalibrated by measurement of electrical resistance at 22° C. and 65° C.under constant voltage; intermediate temperatures are estimated bylinear interpolation.

II. Channel Treatment

Prior to performing microdroplet motion and biological reactions, thechannels are preferably treated by washing with base, acid, buffer,water and a hydrophilicity-enhancing compound, followed by a relativelyhigh concentration solution of non-specific protein. In a preferredembodiment, the channels are washed with approximately 100 μl each ofthe following solutions in series: 0.1N NaOH; 0.1N HCl; 10 mM Tris-HCl(pH 8.0), deionized H₂O, Rain-X Anti-Fog (a hydrophilicity-enhancingcompound commercially available from Unelko Corp., Scottsdale, Ariz.),and 500 μg/μl bovine serum albumin (non-specific protein commerciallyavailable in restriction enzyme grade from GIBCO-BRL). The wafer wasplaced on a stereoscope stage (Olympus SZ1145), and the contact pads forthe heating elements were connected to a regulated power supply. Heatingoccurred by passing approximately 30 volts through the element in shortpulses and observing the movement rate of the droplets. A detectablereduction in droplet volume from evaporation was noted in eachexperiment, usually of less than 30%. Droplet movement was recorded witha Hamamatsu video camera on videotape.

III. Channel Treatment For Hydrophobic Regions

In one embodiment of the device of the present invention (FIG. 8A), thedevice comprises a glass top (810A) bonded to a silicon substrate (810B)containing the heater (891), the contact pad (892) and the resisitivetemperature detector (893). The glass side has channels and chambersetched into it. FIG. 8A shows the inlet (820) and overflow (830) ports,a gas vent (870) and a air chamber (880).

Heaters and Resisitive Temperature Detectors

The fabrication process for the heater and temperature detector (FIG.8B) begins by using Silicon water (p-type, 18-22 alun-cm, boronconcentration˜10¹³ cm³) as a substrate for growth of SlO₂ thermal oxide(1 μm) (STEP 1). A 0.5 μm metallic Aluminum film is electron beamdeposited. Photoresis PR 1827 is applied and spun at 4000 rpm for 30seconds, patterned (metal 1) and developed. The exposed aluminum isetched in Aluminum etchant and the photoresist stripped to define themetal heater (STEP 2).

Photoresist is spun again and a second lithography is done (metal 2). A0.15 μm layer of platimun (“Pt”) is electron beam deposited. A 0.03 μmthick Titanium metal layer (electron beam deposited) is used as theadhesion layer. The resist and the overlying metal is lifted off bydevelopment using Microposit 1112A remover in solution (Shipley Co.).This Platinum metal will be used as the resistive thermal detector.Next, 0.7 μm of Low Temperature Oxide (LTO) of silicon is deposited toact as the barrier layer and the dydrophilic substrate (STEP 4). A thirdlithography is done and the LTO is etched in Buffered Hydrofluoric Acidto open contacts to the metal contact pads. The further processing stepsare done to pattern hydrophobic regions onto the hydrophilic siliconoxide surface.

Hydrophobic Patterning of Silicon Oxide Substrate

A 0.1 μm layer of Chromium metal is electronbeam deposited on theprocessed water. Photoresist PR 1827 is applied and spun at 2000 rpm for30 seconds. The resist is patterned (SAM mask) and developed. Theexposed Chromium metal is etched in Chromium etchant to expose thesilicon oxide and the photoresist is then stripped off (STEP 5). Thesamples are then cleaned in Acetone, Isopropyl Alcohol and DI water for10 minutes each, air dried and oven dried at 100° C. for 5 minutes. Thesamples are then put in 1 wt % octadecyltrichlorosilane (OTS) solutionin Toluene for 15-30 minutes. OTS deposits on the samples as a SelfAssembled Monolayer (SAM) (STEP 6). The samples are then rinsed inToluene, Isopropyl alcohol and DI water for 5 minutes each, and thenoven dried (100° C., 5 minutes). Next, they are put in Chromium etchantto remove the Chromium layer below. The SAM on the Chromium metal getslifted off as a result of this. The samples were then rinsed in DI waterand air dried, resulting in regions of intact hydrophobic regions on ahydrophilic oxide substrate (STEP 7). Heater elements and RTDs have alsobeen fabricated on a quartz substrate. The fabrication steps are similarto that of the silicon processing steps.

Glass Channel and Chamber Fabrication

The channel and the chamber fabrication (FIG. 8C) begins by depositing0.4 μm metallic layer of Gold (Electron beam deposition) on the surfaceof 500 μm thick glass water (Dow Corning 7740) (STEP 1). A 0.06 μm layerof chromium is used as the adhesion layer. Photoresist is applied andpatterned using glass mask 1 and developed (STEP 2). The metal layersare etched in gold etchant (Gold Etchant TFA, Transene Co.) and Chromiumetchant (CR-14, Cyantec Inc.). The accessible glass is then etched in asolution of freshly prepared hydrofluoric and nitric acid (7:3, v/v).The etch rate is approximately 5 μm/min and the etch depth isconveniently measured using a surface profilometer. The metal layers areremoved (STEP 3) and the wafer rinsed in DI water, air dried and ovendried at 100° C. for 20 minutes. The following processing steps are donefor patterning hydrophobic regions onto the glass surface.

Hydrophobic Patterning of Glass Substrate

A 1.5 μm thick Aluminum layer was electron beam deposited, covering theetched channels and chamber (STEP 4). A thick photoresist (AZ 4620) isapplied and spun at 750 rpm for 50 seconds (STEP 5). The resist ispatterned (SAM Mask) and developed. The exposed Aluminum is etched inaluminum etchant. The photoresist is stripped off (STEP 6) in hot PRS2000 (J. T. Baker). The samples are then cleaned in Acetone, Isopropylalcohol and DI water for 5 minutes each and the water dried off in a100° C. oven of 10-15 minutes. The samples are then dipped in a 1% OTSsolution in Toluene for 10-15 minutes (STEP 7). The SAM deposition wascarried out in a Chemical hood. The samples were then rinsed in Toluene,Isopropyl Alcohol and DI water for 5 minutes each. Next, they were putin Aluminum etchant until all metallic aluminum was removed (STEP 8).The samples were then rinsed in DI water and air dried. For the deviceswith the inlet from the top, holes were drilled by electrochemicaldischarge drilling.

The glass side was then aligned on top of the silicon side and thenbonded together using optical adhesive (SK-9 Lens Bond, SumersLaboratories, Fort Washington, Pa.). The bond was cured under anultraviolet light source (365 nm) for 24 hours.

IV. Component Design

The present invention contemplates one or more gel electrophoresismodules as a component of the microscale device. Theoretical andempirical research has indicated that reducing the thickness of theelectrophoresis channel leads to improved resolution. Thinner gelsdissipate heat more readily and allow higher voltages to be used, withconcomitant improvements in separation. The position and width of theelectrophoresis detector are also critical to the ultimate resolution ofthe electrophoresis system. A micromachined electronic detector, such asa photodiode, placed in the underlying silicon substrate can be lessthan one micron from the gel matrix and can have a width of 5 microns orless. Since the gel length required for the resolution of two migratingbands is proportional to the resolution of the detector, theincorporation of micron-width electronic detectors can reduce the totalgel length required for standard genotyping by at least an order ofmagnitude.

To demonstrate that standard gel electrophoresis can operate inmicron-diameter channels, modules were fabricated using etched glasschannels identical to FIG. 6B and fluorescent-labeled DNA (YOYOintercalating dye). Polyacrylamide gel electrophoresis of a complex DNAmixture is shown in FIG. 9A in a channel 500 μm wide and 20 μm deep. Theelectrophoresis was performed with the positive electrode to the rightand the DNA sample applied at the left. The white vertical line is thegel-to-buffer interface. The DNA sample (BluescriptKS digested withMspI) is labeled with intercalating UV-fluorescent dye (YOYO-1) and isvisualized under incandescent light. Separation of the component bandsis clearly visible less than 300 μm from the buffer reservoir-to-gelinterface. The high resolution of the detector (in this case, amicroscope) allowed the use of an unusually short gel, resolving severalclosely eluting bands.

The present invention contemplates an electrophoresis unit thatintegrates a micromachined channel and an electronic DNA detector. Thechannel is constructed using a sacrificial etch process on a singlesilicon wafer rather than the bonded surface-etch method describedearlier. In the sacrificial etch technique, the channel configuration ispatterned by depositing on the wafer surface an etch-sensitive material(phosphosilicate glass, SiO₂.P_(x)) with a thickness equivalent to thedesired channel height. A triple-layer overlay of plasma-enhancedchemical vapor deposited silicon nitride, undoped polycrystallinesilicon, and silicon nitride (Si_(x)N_(y)/polySi/Si_(x)N_(y)) completelycovers the sacrificial material with the exception of small access holeson the top or sides. A selective liquid etch removes the sacrificiallayer material, but not the overlay or the underlying substrate. Thesacrificial etch technique results in a complete channel being formeddirectly on the substrate containing the electronic components (FIGS. 6Cand 6D). The 3 μm deep channel has two buffer reservoirs on either endwith integral phosphorus-doped polycrystalline silicon electrodes. Thechannel height formed by this technique (˜3 μm) is considerably smallerthan the height of the bonded structures due to the limitations of thesacrificial layer deposition and the strength of the overlying layer.Note that, for these channel dimensions, liquid drops would have volumeson the order of picoliters.

FIG. 9B is photomicrograph of a set of four doped-diffusion dioderadiation detector elements fabricated on a silicon wafer. For eachelement, the three parallel dark lines define the diffusion regions ofthe central the detector flanked by the guard ring shielding electrodes.The diffusion regions are approximately 300 μm long and 4 μm wide.

A radiation detector, consisting of a 10 μm wide “p-n”-type diode with a5 μm wide guard ring around the outer edge, is fashioned directly intothe silicon substrate underneath the channel. In this implementation, anintegral radiation detector was chosen because of (i) high sensitivity(a single decay event), (ii) small aperture dimensions, and (iii)well-know fabrication and response characteristics. On thiselectrophoresis system, a 1 cm long, 3 μm thick gel is able to performas separation on a 80 and a 300 base-pair fragment of DNA. It should benoted that this diode, although currently configured for high-energybeta particle detection, can also operate as a photon detector. Withproper wavelength filters and light sources, detection of fluorescenceemission may be accommodated with a similar device.

Radiation detectors were prepared as follows. A 200 ½-cm, <100>, floatzone, boron-doped, p-type silicon wafer was used as a substrate.Diffused layers of phosphorus (5×10¹⁴ cm⁻²) and boron (1×10¹⁵ cm⁻²) wereion-implanted onto the sample in lithographically-defined regions;thermal silicon oxide was grown (0.2 μm at 900° C.) over the, wafer; andcontact holes were etched to the diffusion layer using bufferedhydrofluoric acid solution (5:1). A 3.3 μm layer of Microposit 1400-37photoresist was patterned to define the metal pads; 50 nm chromiumfollowed by 400 nm gold was evaporated over the resist; and themetallization lifted off the regions retaining the resist. A layer ofMicroposit 1813 photoresist was applied across the wafer and baked for110° C. for 30 minutes to form an aqueous solution barrier. Radioactivephosphorus (³²P) decay events could be detected using a sample oflabeled DNA in PCR reaction buffer placed on the photoresist layer. Thedetector was connected to a charge-sensitive preamplifier (EV-Products550A), followed by a linear shaping amplifier and a standardoscilloscope.

FIG. 9C shows an oscilloscope trace of output from the radiationdetector showing individual decay events from ³²P-labeled DNA. Theaqueous DNA sample was placed directly on the detector and sampled for30 seconds. The screen is displaying a vertical scale of 0.5V/divisionand horizontal scale of 20 μsec/division.

Experimental

The following examples serve to illustrate certain preferred embodimentsand aspects of the present invention and are not to be construed aslimiting the scope thereof.

In the experimental disclosure which follows, the followingabbreviations apply: eq (equivalents); M (Molar); VM (micromolar); N(Normal); mol (moles); nmmol (millimoles); gmol (micromoles), nmol(nanomoles); gm (grams); mg (milligrams); μg (micrograms); L (liters);ml (milliliters); μl (microliters); cm (centimeters); mm (millimeters);μm (micrometers); nm (nanometers); ° C. (degrees Centigrade); Ci(Curies); MW (molecular weight); OD (optical density); EDTA(ethylenediamine-tetracetic acid); PAGE (polyacrylamide gelelectrophoresis); UV (ultraviolet); V (volts); W (watts); mA(milliamps); bp (base pair); CPM (counts per minute).

EXAMPLE 1

This example describes approaches to the problem of forming a moisturebarrier over electrical elements of the microscale device. Initialprototypes employed 5000 angstroms of aluminum and covered it with PECVDSiO_(x). Upon testing, it was determined that the liquids werepenetrating this later and destroying the aluminum heating elements.

Without clear evidence what was causing this problem, it washypothesized that the step height of the aluminum was causing cracks inthe passivation layer (the oxide). In order to alleviate the crackingproblem, a layer of Si_(x)N_(y) was tried between two layers of SiO_(x),with the thought that the additional thickness would overcome thecracking caused by the step height. It did not.

As a follow-up approach, a thinner layer (500 angstroms) of aluminum wastried. This gave {fraction (1/10)}th the step height of the originalprototype devices. On top of this aluminum, a triple layer of SiO_(x),Si_(x)N_(y), and SiO_(x) was employed. Moreover, the process for makingthe Si_(x)N_(y) layer was changed to one which would give a more denselayer. This appeared to solve the problem. However, the thinner layer ofaluminum created a higher resistance which was not acceptable. It wasdetermined that one needed a way to generate thicker layers of aluminumfor lower resistance, yet keep the surface relatively smooth (planar).An etch back process was used (now called “the inlay process”) toaccomplish the task. By etching back into a layer of SiO_(x) depositingaluminum in the resulting cavity, then stripping the resist mask, asurface was obtained with a step height low enough to prevent crackingof the passivation layers.

It was also discovered that the metal bonding pads were not adheringwell to the initial PECVD SiO_(x) layer. To overcome the problem, theprocess was modified by using a wet thermal SiO₂ layer.

EXAMPLE 2

This example describes approaches to enhancing droplet motion by surfaceto treatment. In this regard, the principle of using surface tension tocause droplets to move may be applied to either hydrophilic orhydrophobic surfaces. Glass, for instance, is naturally hydrophilic witha near zero contact angle with water. Because the oxide coating of thepresent invention is made principally of the same material as glass, itwas expected that the devices would also exhibit near zero angles. Itwas discovered, however, that the actual construction materials hadcontact angles far from zero, thus enhancing the effects of contactangle hysteresis (discussed in greater detail in Example 3). Forinstance, water gave a contact angle (static) of ˜42° on polyamide, ˜41on SiO₂ (major component of most glasses), ˜62° on silicone spray. Toenhance the surface effectiveness, several treatment processes for bothhydrophilic and hydrophobic surfaces were tried, as described below.

To improve the hydrophilicity of a surface, several cleaning procedureswere tried. It has been reported that surface contamination and/orroughness can reduce the hydrophilicity of surfaces. Therefore, a highconcentration chromic acid cleaning, a high concentration sulfuric acidcleaning, a baking procedure (to 600° C. for 8 hrs. to burn offcontaminates), and surface coatings were tried. The acid cleaningprocedures were not as effective as the baking procedure; however,neither proved to be compatible with the devices since the concentratedacids would attack the aluminum pads and the high temperature could pealthe aluminum (melting pt. ˜660° C.) or break the adhesive bond betweenthe heater chip and the channel.

Rain-X antifog (commercially available) as a treatment was observed towork. This is a surface treatment which makes surfaces hydrophilic.Although, the resulting surfaces may not be 0°, by using this coatingthe entire surface gets treated giving a uniform surface for thedroplet. Experimentally, it was found that Rain-X antifog treatmentsgreatly enhanced droplet motion experiments using heat. Another suchtreatment which was tested but which did not work was a material calledSilWet. This material is used in the agriculture industry for enhancingthe wetting of plants with agricultural sprays.

To obtain hydrophobic surfaces, the present inventors tried coatingcapillaries with Rain-X and silane treatments. Neither of these gaveangles much greater than 90°, therefore, would not work with thismechanism. These treatments would have to have given angles ˜180° to beuseful for hydrophobic studies of motion. Eventually, it was discoveredthat one could apply a teflon coating that was sufficiently hydrophobicto possibly warrant future tests.

EXAMPLE 3

This example describes approaches to droplet motion by heat treatment.As noted previously (above), the contact angle on the advancing end of aliquid droplet in motion (known as the advancing contact angle) isgreater that the that on the receding end (receding contact angle). Inthe case of a hydrophilic surface—such as water on glass—this tends tocreate a back pressure countering attempts at forward motion by heatingthe back side of a droplet. This is best shown by a simple modeldescribing laminar flow through a channel.

Average Flow Through a Circular Channel: {v} = −ΔP*[R²/(8μL] where: Δ =value at back - value at front end of droplet ΔP = (1/R)*(ΔG) = pressuredifference between droplet ends ΔG = change in surface tension betweenthe ends of the droplet. R = channel radius L = droplet length μ =viscosityAlso, for water, ΔG=−constant*ΔT, where temperature increases lower thesurface tension of most liquids (constant=0.16 dyn/cm for water).

Therefore: {v} = −(ΔG)*(1/R)*[R²/(8μL)] = [−0.16*ΔT*R/(8μL)] where: ΔT =T_(back)-T_(front) giving: {v} = [0.16*R/(8μL)] * (T_(back)-T_(front)).giving:

-   -   (v)=[0.16*R/(8 μL)]*(T_(back)−T_(front))        This expression indicates that any heating on the back end of        the droplet (if the front remains at a lower temperature) will        cause the liquid droplet to move. This was not the case        experimentally, however. By way of studies using glass        capillaries, it was found that there was a minimum temperature        difference required to move the droplet. This effect is believed        to be the result of contact angle hysteresis (CAH). In CAH, the        advancing contact angle is greater than the receding contact        angle resulting in a sort of back pressure which must be        overcome to achieve droplet movement. CAH occurs when the        interface is placed in motion (dynamic angles). To account for        this effect, it was included in a steady-state (1D) model for        flow. For instance, if the advancing angle is 36° and the        receding angle is 29° (with the front of the droplet being 25°        C.), then the back of the droplet would need to be heated to        ˜60° C. for a 1 mm long droplet in a 20 μm high channel. This is        just one example situation.

It was discovered experimentally, however, that the channel dimensionand fluid parameters (other than surface tension) do not affect whetheror not the droplet will move. They do determine the magnitude of motion(if it occurs). What does determine whether motion will occur or not isthe following inequality:G _(front) /G _(back)>(R _(front) /R _(back))*(cos β_(back)/cosβ_(front))where:

-   -   β=contact angle.

The present calculations suggest that a ˜35° C. difference between thefront and back of a droplet should be sufficient to initiate dropletmotion in a system with advancing angles of 36° and receding angles of29° in a 20 μm high channel. Experimental testing of actual deviceshowever, showed that the front of the droplet heats relatively quicklythus reducing the temperature difference needed for movement between thefront and the back of the droplet. This effect required us to use highervoltages to obtain droplet motion. Voltages typically in the range of˜30° Volts were found to be required to obtain motion. Furtherexperiments showed that the resulting temperature difference was ˜40° C.between the front and back of the droplet thus corroborating the initialdetermination of the requirements.

Discrete droplet motion in a micromachined channel structure usingthermal gradients is demonstrated in the videorecorded images of FIGS.6A, 6B, 6C, and 6D. The device consists of a series of aluminum heatersinlaid on a planar silicon dioxide substrate (similar to the structureshown in FIG. 2) and bonded by glue to a wet-etched glass channel (20 μmdepth, 500 μm width). Liquid samples were manually loaded into the twochannels on the left using a micropipette. Heating the left interface ofeach droplet propels it toward the intersection of the channels. At theintersection, the droplets meet and join to form a single largerdroplet. Note that, since the channel cross-section is 20 μm×500 μm, thevolume of each of these droplets can be calculated from their lengthsand is approximately 50 nanoliters.

The heaters along the entire surface of the channel shown in FIG. 6allow it to be used as a thermal reaction chamber in addition to adroplet-motion device. The upper droplet in the figure contains a DNAsample, while the lower contains a restriction digest enzyme (TaqI) anddigestion buffer. Following sample merging, the combined droplet wasmaintained at 65° C. for 30 minutes using the integral heaters andtemperature sensors. The completed enzymatic reaction was confirmed byexpressing the droplet from the right end of the channel and loading itonto a capillary gel electrophoresis system with a laser-inducedfluorescence detector. The chromatogram produced by the silicon-devicesample was similar to chromatograms generated from DNA digests runs in astandard polypropylene microreaction vessel (not shown).

EXAMPLE 4

This example describes various approaches for bonding channels to thesubstrate which contains circuitry for heating and temperature sensingof the device of the present invention (see discussion of two-partconstruction, above). First attempts involved Polyamide; regularpolyamide was unsatisfactory in that it was found the two pieces wouldnot stick together.

Follow-up attempts involved a photo-definable Polyamide. This produced asticky surface, but would not give a perfect seal along the channel. Itwas discovered that the solvents released during the final bakingprocess were causing pockets in the polyamide layer. An adhesion layerwas needed which would seal by ‘curing’ and not release solvents.

Several different epoxies and glues were investigated, as listed below.

Adhesive Form Dries Texture Comments 1. Dymax UV Glue Gel Clear RubberyCures on UV exposure. 2. Carter's Rubber Goo Yellow/Clear Rubbery Driesquickly and Cement stringy when thinned. 3. Borden's Krazy Liquid ClearHard Thin, dries on first Glue contact. 4. UHU Bond-All Gel/Goo ClearHard Dries quickly and stringy when thin. 5. Dennison Paste Clear HardWill not flow on Permanent Glue applying. Stick 6. Elmer's Glue-AllThick Liquid White Hard Slow drying. (Borden) 7. Liquid Nails Thin PasteWood-like Hard Thick, dries quickly when thinned. 8. Devcon 5-Minute GelYellow/Clear Hard Thick, cures on about Epoxy 5 min. 9. Scotch Double-Tape Clear Rubbery Tape. Stick Tape 10. Dow Corning Thick Gel FrostySoft Seals but does not High Vacuum bond. Grease 11. Nujol MineralLiquid Clear Runny Neither seals (doesn't Oil (Perkin spread on glass)nor Elmer) bonds. 12. Household Goop Gel/Goo Clear Rubbery Contactcement which dries stringy. 13. Permatex Gel/Goo Yellow/Clear RubberyDries quickly and Weather Strip stringy when thinned. Cement 14. ThickGel Super Gel Clear Hard Does not cure on Glue contact but does quickly.15. DAP Weldwood Goo Orange/Clear Rubbery Contact cement which ContactCement gets stringy when thinned. 16. Scotch (3M) Thin Goo Yellow/ClearRubbery Spray. ‘Gooey’ but Photo Mount not stringy. Spray Adhesive 17.Silicone Resin Liquid Clear Smooth Spray. Dries to thin, (spray) Lacquerclear, and sealed (GC Electronics) coating.

A preferred glue was a UV cured glue, although the process of applyingthe UV glue is tedious and requires some practice to avoid putting theglue in places where it does not belong, e.g., in the channels.

Hydroxide bonding and screen printing of bonding substances was alsoattempted. Another option was glass tape, but the high temperaturesrequired to melt the tape appeared to be too high for the presentdevices.

EXAMPLE 5

This example describes a nucleic acid amplification reaction on asilicon-based substrate. The established DNA biochemistry steps for PCRoccur within physiological conditions of ionic strength, temperature,and pH. Thus, the reaction chamber components have design limitations inthat there must be compatibility with the DNA, enzymes and otherreagents in solution.

To assess biocompatability, components were added to a standard PCRreaction. The results (see FIG. 10) indicated that crystalline siliconmay not be the ideal material for biological compatibility. Given theseresults, it may be desirable to modify the surface of the micromachinedsilicon substrate with adsorbed surface agents, covalently bondedpolymers, or a deposited silicon oxide layer.

To form a biologically compatible heating element, the present inventorsbegan by coating a standard silicon wafer with a 0.5 μm layer of silicondioxide. Next, a 0.3 μm deep, 500 μm wide channel was etched into thesilicon oxide and gold or aluminum was deposited (0.3 μm thick). Thisinlay process results in a relatively planar surface and provides a basefor deposition of a water-impermeable layer. The impermeable layer ismade by a sequence of three plasma enhanced vapor depositions: siliconoxide (SiO_(x)), silicon nitride (Si_(x)N_(y)), and silicon oxide(SiO_(x)). Since the materials are deposited from the vapor phase theprecise stoichiometries are not known. A thin metal heater design wasused for this device rather than the doped-silicon resistive heaterspreviously demonstrated for micromachined PCR reaction chambers, sincethe narrow metal inlay allows viewing of the liquid sample through atransparent underlying substrate, such as glass or quartz. Also, the useof several independent heating elements permits a small number tooperate as highly accurate resistive temperature sensors, while themajority of elements are functioning as heaters.

A device fabricated with metal resistive heaters and oxide/nitride/oxidecoating was tested for biological compatibility and temperature controlby using PCR amplification of a known DNA template sample. The reactionwas carried out on the planar device using twenty microliters of PCRreaction mix covered with mineral oil to prevent evaporation. Thereaction mixture was cycled through a standard 35-cycle PCR temperaturecycling regime using the integral temperature sensors linked to aprogrammable controller. Since the reaction volume was significantlylarger than intended for the original heater design, a polypropylenering was cemented to the heater surface to serve as a sample containmentchamber. In all test cases, the presence of amplified reaction productsindicated that the silicon dioxide surface and the heater design did notinhibit the reaction. Parallel amplification experiments performed on acommercial PCR thermocycler gave similar results. A series of PCRcompatibility tests indicated that the reaction on the device is verysensitive to controller settings and to the final surface material incontact with the sample (not shown).

From the above it should be evident that the present invention can beadapted for high-volume projects, such as genotyping. The microdroplettransport avoids the current inefficiencies in liquid handling andmixing of reagents. Moreover, the devices are not limited by the natureof the reactions, including biological reactions.

EXAMPLE 6

In this example, a test structure is fabricated (FIG. 11). The teststructure is very simple (FIG. 11). The main part is constructed from atwo mask process with five layers of materials on top of the Sisubstrate. Proceeding from the lowest to the uppermost layer, the SiO,serves as an insulator between the Si substrate and the other metallayers, which function as solder pads and heating elements. The Ti layer(250A) is for adhesion of Ni. The layers of Ni (1000 A) and Au (1000 A)act as a diffusion barrier for the solder. The Au layer also serves as awettable pad. Finally, the layer of solder is for bonding two substratestogether. The solder will melt by heating the metal layers. Anothersubstrate that will be bonded has the same construction except for thesolder.

A thermo-pneumatic microvalve is utilized in the test structure. Theschematic and process flow of the microvalve is shown in FIGS. 12A-J. Acorrugated diaphragm is chosen for its larger deflection and highersensitivity. The diaphragm (side length=1000 um, thickness=3 um, bosssize length=500 um boss thickness=10 um) has a deflection of 27 um at anapplied pressure of 1 atm. This applied pressure is generated by athermo-pneumatic mechanism, which provides a greater actuation force. Apressure of 1 atm is generated in the cavity between the diaphragm andglass by Freon-11 when it is heated 11° C. above room temperature. Asset forth in FIGS. 12A-J, ten masks are anticipated to fabricate themicrovalve.

FIG. 9 a shows a portion of a silicon substrate 10, which is a p-type(100)-oriented Si wafer of normal thickness and moderate doping (>1 cm).The preferred wafer thickness, however, is ordinarily a function of thewafer diameter. The upper surface 12 of the silicon wafer containingsubstrate 10 is lapped, polished and cleaned in the normal and acceptedmanner. Isotropic etching using reactive ion etching (RIE) forms thediaphragm corrugations 14 with photoresist as the masking material.

FIG. 12B shows the definition of deep boron diffusion areas 16 to formthe rims, center bosses, inlet and outlet holes of the finished device.FIG. 12C shows the deposition of shallow boron diffusion areas 18 toform a diaphragm. The various metal layers, including solder 20, arethen deposited. The deep and shallow boron diffusion processes definethe shape of the diaphragm and the etch-stop for the dissolved waferprocess.

Following this, FIG. 12D shows the definition of oxide layer 22 to serveas insulator of the solder of the finished device. Ti adhesion/Ni/Aubarrier and wettable pads 24 are then deposited as shown in FIG. 12E.The solder mold 26 of Ni and photoresist is then defined as shown inFIG. 12F) and the first Ni channel 28 is created bysurface-micromachined using photoresist as sacrificial layers. The Nichannel hole is defined using EDP to remove the sacrificial layers, anddefine an channel hole 30 (FIG. 12G).

A second Ni channel 32 is defined by Ni and photoresist as set forth inFIG. 12H, and inlet 34 and outlet 36 holes are defined using EDP toremove the sacrificial layers (FIG. 121).

Lastly, a Ti/Pt heater in glass 38 is anodically bonded to the siliconsubstrate (FIG. 12J). Freon-11 fills the cavity through a hole (notshown) in the glass substrate. This hole is created from a diamond drillbit and sealed with epoxy.

EXAMPLE 7

In this example, a low melting point solder was intended to be utilizedin the test structure. Because a universally useful solder-sealedmicrovalve will be used in a gas phase microanalytical system, it is notdesirable to use a high melting point (m.p.) solder (>200° C.), whichmight affect the gas properties. In addition, a high m.p. solder mayaffect other components on the device, such as integrated circuits, andincrease power consumption. As a result, low melting point solder isrequired. Bismuth-bearing solders have the lowest m.p.'s of 47-138° C.However, when a test structure was dipped into a pool of solderbelonging to this group, all the metal layers dissolved into thesolution of solder. Moreover, this solder was not selective in wettingthe surface of the test structure.

EXAMPLE 8

In light of the results of the experiment set forth in Example 7, anattempt was made with commonly available 60:40 Sn:Pb solder (m.p. 183°C.). When the test structure was dipped into a solution of this solder,the metal layers remained intact. Furthermore, these layers demonstratedexcellent wettability for the solder, i.e. the solder was confined onlyto the areas of metals.

EXAMPLE 9

In this example, a device and method for blocking fluid flow in achannel is described. FIG. 13 sets forth a test schematic for theseembodiments. 60:40 Sn:Pb solder 40, associated with a heating element42, is placed within a side channel 44. The heating element 42 at leastpartially liquifies the solder 40 and air flow 46 moves the liquifiedsolder from the side channel into a main channel 48 and cooled, blockingthe main channel.

EXAMPLE 10

In this example, a device, which was fabricated using lift-off methoddescribed above to pattern hydrophobic regions on glass and siliconsubstrates, was testing for the separation of water droplets. For thedevice, a patterned metallic thin film was used to expose regions thatwere chosen to be made hydrophobic on a hydrophilic substrate. Chromium,Gold or Aluminum was used as the metal layer; the choice of the metalbeing based on process compatibility with other processing steps andstep height coverage of the etched channels.

Line widths as narrow as 10 μm were patterned on silicon substratesusing the methods of the present invention. FIG. 14 shows water dropsseparated by lines of hydrophobic (A) and hydrophilic regions (B)patterned by this new technique (the width of the hydrophilic line inthe middle is 1 mm). The contact angle of water on the OTS (SAM) coatedsilicon oxide surface was measured to be approximately 110°.

One can also define hydrophobic regions in etched channels in glass byperforming the lithography using a thick resist. It was found empricallythat cleaning of the substrates prior to immersion in the OTS (SAM)solution is important; improper cleaning results in films that partiallycovers the surface.

EXAMPLE 11

The results of Example 10, above, demonstrate that hydrophobic andhydrophilic patterns enable one to define and control the placement ofaqueous liquids, and more specifically microdroplets of such liquids, ona substrate surface. FIGS. 15A, 15B, and 15C show a simple use of thispatterning technique to split a liquid droplet into multiple liquiddroplets. A concentric pattern of alternating hydrophobic (dark) andhydrophilic (white) sectors was imparted to a silicon substrate (FIG.15A; the diameter of the circle is 1 cm) using the methods of thepresent invention as described above. A water drop was placed on thepattern (FIG. 15B) and the excess water pulled away using a pipet,resulting in multiple drops separated from each other (FIG. 15C).

EXAMPLE 12

In this example, experiments are describe to position a water frontinside a channel using straight channels (depth ranging from 20-40 μmand width between 100-500 μm) with a 500 μm wide hydrophobic region (orpatch) patterned a few millimeters away from the side inlet. Water wasplaced at the inlet using a sequencing pipette (Sigma, least count 0.5μl) and was drawn into the channel by surface forces. The water frontstopped at the hydrophobic patch if a controlled amount of liquid wasplaced at the inlet. However, if the channels were overloaded, theliquid would tend to overrun the hydrophobic patch. This behavior wasprominent in the channels with smaller cross-section.

To eliminate the over-running of the liquid over the patches, anoverflow channel was introduced in the design to stop the water runningover the hydrophobic patch (such as that shown in FIGS. 3A and 3B). Thedimensions of the channels varied in depth and width as before. Waterplaced at the inlet is drawn in and splits into two streams at theintersection point. The two fronts move with almost equal velocity untilthe front in the main channel reaches the hydrophobic patch. The frontin the main channel stopped at the hydrophobic patch; however, the otherfront continued to move to accommodate the excess injected water. Usingthis overflow channel design, one can successfully stop aqueous liquidsfor the full range of variation in channel dimensions.

EXAMPLE 13

FIGS. 16A-J are schematics and photographs of one embodiment of thedevice (910) of the present invention (in operation) utilizing a heater.FIGS. 16A and 16F show that liquid placed at the inlet (920) stops atthe hydrophobic interfaces, and more specifically, stops at theliquid-abutting hydrophobic region (940). The inlet (920) and overflow(930) ports were blocked or heavily loaded with excess liquid to ensurethat the pressure generated acts only in the direction away from theinlet holes. The heater resistor (991) was actuated by an appliedvoltage. The flow of current caused resistive heating and subsequentlyincreases the air temperature in the chamber (980) and, therefore, thepressure. After the pressure builds up to a particular value, amicrodrop splits and moves beyond the hydrophobic patch (FIGS. 16B and16G). The drop keeps moving as long as the heater is kept on; the dropvelocity decreases as it moves further away. While it is not intendedthat the present invention be limited by the mechanism by which thistakes place, it is believed that the added volume (the volume by whichthe drop has moved) brings about a decrease in the pressure.

To stop or block the moving drop at a location, two strategies can beemployed. In the first method, the inlet and overflow ports were openedto the atmosphere and the heater was slowly turned off. The temperatureinside the chamber falls quickly to around room temperature, therebyreducing the pressure inside the chamber. The water from the inlet flowsinto the chamber to relieve the pressure (FIGS. 16C and 16H). In thesecond method, a hydrophobic vent was placed away from the chamber tothe right. As soon as the moving drop goes past the hydrophobic vent(FIGS. 16D and 16I), the drop stops moving farther (FIGS. 16E and 16J).Cooling the chamber to room temperature at this instant will cause airto flow back through the vent to relieve the low pressure in thechamber.

From the above, it should be clear that the compositions, devices andmethods of the present invention permit on-chip actuation using etchedchambers, channels and heaters. There is no requirement for mechanicalmoving parts and the patterns are readily fabricated. While theoperations described above have been for simple designs, the presentinvention contemplates more complicated devices involving theintroduction of multiple samples and the movement of multiplemicrodroplets (including simultaneous movement of separate and discretedroplets).

1. A device comprising first and second side channels attached to amicrodroplet transport channel etched in substrate so as to create firstand second intersections, said first and second side channels havinghydrophobic surfaces said microdroplet transport channel comprising ahydrophobic region and liquid abutting said hydrophobic region, saidliquid extending through said first intersection without entering saidfirst side channel wherein said hydrophobic region is positioned in saidmicrodroplet transport channel between said first and second sidechannels.
 2. The device of claim 1, wherein said microdroplet transportchannel is between 5 and 20 μm in depth and between 20 and 1000 μm inwidth.
 3. A device comprising first and second side channels attached toa microdroplet transport channel so as to create first and secondintersections, said first and second side channels having hydrophobicsurfaces, said microdroplet transport channel comprising i) first andsecond ends, said first end comprising a liquid inlet port ii) ahydrophobic region disposed within said microdroplet transport channelbetween said first and second ends, and iii) liquid extending from saidinlet port through said first intersection, without entering said firstside channel, and abutting said hydrophobic region.
 4. The device ofclaim 3, wherein said device is fabricated from a glass, quartz orsilicon substrate.
 5. The device of claim 3, wherein said microdroplettransport channel is between 5 and 20 μm in depth and between 20 and1000 μm in width.